def test_create_functions(setup_folder):
"""
Test create root zarr, create position subfolders, and switching between
position substores
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test',
hcs=True,
hcs_meta=hcs_meta,
verbose=False)
writer.create_zarr_root('test_zarr_root')
assert (writer.sub_writer.root_path == folder +
'/Test/test_zarr_root.zarr')
assert (writer.sub_writer.store is not None)
# Check that the correct hierarchy was initialized
cnt = 0
for row in hcs_meta['plate']['rows']:
for col in hcs_meta['plate']['columns']:
for fov in range(1, 3):
path = f'{row["name"]}/{col["name"]}/FOV{fov}'
assert (isinstance(writer.sub_writer.store[path], zarr.Group))
assert (writer.sub_writer.positions[cnt] == {
'name': f'FOV{fov}',
'row': row["name"],
'col': col["name"]
})
cnt += 1
def test_create_functions(setup_folder):
"""
Test create root zarr, create position subfolders, and switching between
position substores
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test',
hcs=False,
hcs_meta=None,
verbose=False)
writer.create_zarr_root('test_zarr_root')
assert (writer.sub_writer.root_path == folder +
'/Test/test_zarr_root.zarr')
assert (writer.sub_writer.store is not None)
assert (isinstance(writer.sub_writer.store['Row_0'], zarr.Group))
# Check Plate Metadata
assert ('plate' in writer.sub_writer.plate_meta)
assert ('rows' in writer.sub_writer.plate_meta.get('plate').keys())
assert ('columns' in writer.sub_writer.plate_meta.get('plate').keys())
assert ('wells' in writer.sub_writer.plate_meta.get('plate').keys())
assert (len(writer.sub_writer.plate_meta.get('plate').get('wells')) == 0)
assert (len(writer.sub_writer.plate_meta.get('plate').get('columns')) == 0)
assert (len(writer.sub_writer.plate_meta.get('plate').get('rows')) == 1)
# Check Well metadata
assert ('well' in writer.sub_writer.well_meta)
assert (len(writer.sub_writer.well_meta.get('well').get('images')) == 0)
def test_constructor_existing(setup_folder):
"""
Test isntantiating the writer into an existing zarr directory
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test')
writer.create_zarr_root('existing.zarr')
writer_existing = WaveorderWriter(folder + '/Test/existing.zarr')
assert (writer_existing.sub_writer.root_path == folder +
'/Test/existing.zarr')
assert (writer_existing.sub_writer.store is not None)
def test_constructor(setup_folder):
"""
Test that constructor finds correct save directory
Returns
-------
"""
folder = setup_folder
writer_def = WaveorderWriter(folder + '/Test',
hcs=True,
hcs_meta=hcs_meta,
verbose=False)
assert (isinstance(writer_def.sub_writer, HCSZarr))
assert (isinstance(writer_def.sub_writer, WriterBase))
z_defocus,
n_media=n_media,
cali=cali,
bg_option=bg_option,
A_matrix=A_matrix,
phase_deconv='3D',
inc_recon='3D',
illu_mode='Arbitrary',
Source=Source,
Source_PolState=Source_PolState,
use_gpu=use_gpu,
gpu_id=gpu_id)
# ### Writer setup
uPTI_file_name = 'uPTI_subFOVs.zarr'
writer = WaveorderWriter(output_path, hcs=False, hcs_meta=None, verbose=True)
writer.create_zarr_root(uPTI_file_name)
data_shape = (1, 9, N_defocus, int(Ns), int(Ms))
chunk_size = (1, 1, 1, int(Ns), int(Ms))
chan_names = [
'f_tensor0r', 'f_tensor0i', 'f_tensor1c', 'f_tensor1s', 'f_tensor2c',
'f_tensor2s', 'f_tensor3', 'mat_map0', 'mat_map1'
]
# append stitching parameters
row_list = (ns // N_space).astype('int')
column_list = (ms // M_space).astype('int')
uPTI_file = zarr.open(os.path.join(output_path, uPTI_file_name), mode='a')
uPTI_file.create_dataset('row_list', data=row_list)
uPTI_file.create_dataset('column_list', data=column_list)
retardance_pr_PT = np.array([((-1)**i) * wo.wavelet_softThreshold(
((-1)**i) * retardance_pr_PT[i], 'db8', 0.00303, level=1)
for i in range(2)])
# ## Visualize reconstructed physical properties of the anisotropic glass target
# ### Reconstructed phase, absorption, principal retardance, azimuth, and inclination assuming (+) and (-) optic sign
# browse the reconstructed physical properties
wo.plot_multicolumn(np.stack([phase_PT[...,44], retardance_pr_PT[0,:,:,44], azimuth[0,:,:,4], theta[0,:,:,44], \
absorption_PT[...,44], retardance_pr_PT[1,:,:,44], azimuth[1,:,:,44], theta[1,:,:,44]]),
num_col=4, origin='lower', set_title=True, size=5, \
titles=[r'phase',r'principal retardance (+)', r'$\omega$ (+)', r'$\theta$ (+)',\
r'absorption',r'principal retardance (-)', r'$\omega$ (-)', r'$\theta$ (-)'])
plt.show()
# save results to zarr array
writer = WaveorderWriter('.', hcs=False, hcs_meta=None, verbose=True)
writer.create_zarr_root('Anisotropic_target_small_processed.zarr')
chan_names = [
'f_tensor0r', 'f_tensor0i', 'f_tensor1c', 'f_tensor1s', 'f_tensor2c',
'f_tensor2s', 'f_tensor3', 'mat_map0', 'mat_map1'
]
uPTI_array = np.transpose(
np.concatenate((f_tensor, mat_map), axis=0)[np.newaxis, ...],
(0, 1, 4, 2, 3)) # dimension (T, C, Z, Y, X)
data_shape = uPTI_array.shape
chunk_size = (1, 1, 1) + uPTI_array.shape[3:]
writer.init_array(0,
data_shape,
chunk_size,
chan_names,
position_name='f_tensor',
def test_write(setup_folder):
"""
Test the write function of the writer
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test',
hcs=True,
hcs_meta=hcs_meta,
verbose=False)
writer.create_zarr_root('test_zarr_root')
data = np.random.randint(1,
60000,
size=(3, 3, 11, 128, 128),
dtype='uint16')
data_shape = data.shape
chunk_size = (1, 1, 1, 128, 128)
chan_names = ['State0', 'State1', 'State3']
clims = [(-0.5, 0.5), (0, 25), (0, 10000)]
dtype = 'uint16'
writer.init_array(0,
data_shape,
chunk_size,
chan_names,
dtype,
clims,
position_name=None,
overwrite=True)
# Write single index for each channel
writer.write(data[0, 0, 0], p=0, t=0, c=0, z=0)
assert (np.array_equal(
writer.sub_writer.store['A']['1']['FOV1']['arr_0'][0, 0, 0], data[0, 0,
0]))
# Write full data
writer.write(data, p=0)
assert (np.array_equal(
writer.sub_writer.store['A']['1']['FOV1']['arr_0'][:, :, :, :, :],
data))
# Write full data with alt method
writer.write(data, p=0, t=slice(0, 3), c=slice(0, 3), z=slice(0, 11))
assert (np.array_equal(
writer.sub_writer.store['A']['1']['FOV1']['arr_0'][:, :, :, :, :],
data))
def test_init_array(setup_folder):
"""
Test the correct initialization of desired array and the associated
metadata
Parameters
----------
setup_folder
Returns
-------
"""
folder = setup_folder
writer = WaveorderWriter(folder + '/Test',
hcs=True,
hcs_meta=hcs_meta,
verbose=False)
writer.create_zarr_root('test_zarr_root')
data_shape = (3, 3, 21, 128, 128) # T, C, Z, Y, X
chunk_size = (1, 1, 1, 128, 128)
chan_names = ['State0', 'State1', 'State3']
clims = [(-0.5, 0.5), (0, 25), (0, 10000)]
dtype = 'uint16'
writer.init_array(0,
data_shape,
chunk_size,
chan_names,
dtype,
clims,
position_name=None,
overwrite=False)
writer.init_array(11,
data_shape,
chunk_size,
chan_names,
dtype,
clims,
position_name='Test',
overwrite=False)
assert (isinstance(writer.sub_writer.store['A']['1']['FOV1'], zarr.Group))
meta_folder = writer.store['A']['1']['FOV1']
meta = meta_folder.attrs.asdict()
array = meta_folder['arr_0']
assert (meta_folder is not None)
assert (array is not None)
assert (array.shape == data_shape)
assert (array.chunks == chunk_size)
assert (array.dtype == dtype)
assert (meta is not None)
assert ('multiscales' in meta)
assert ('omero' in meta)
assert ('rdefs' in meta['omero'])
# Test Chan Names and clims
for i in range(len(meta['omero']['channels'])):
assert (meta['omero']['channels'][i]['label'] == chan_names[i])
assert (meta['omero']['channels'][i]['window']['start'] == clims[i][0])
assert (meta['omero']['channels'][i]['window']['end'] == clims[i][1])
assert (isinstance(writer.sub_writer.store['B']['2']['FOV2'], zarr.Group))
meta_folder = writer.store['B']['2']['FOV2']
meta = meta_folder.attrs.asdict()
array = meta_folder['arr_0']
assert (meta_folder is not None)
assert (array is not None)
assert (array.shape == data_shape)
assert (array.chunks == chunk_size)
assert (array.dtype == dtype)
assert (meta is not None)
assert ('multiscales' in meta)
assert ('omero' in meta)
assert ('rdefs' in meta['omero'])
# Test Chan Names and clims
for i in range(len(meta['omero']['channels'])):
assert (meta['omero']['channels'][i]['label'] == chan_names[i])
assert (meta['omero']['channels'][i]['window']['start'] == clims[i][0])
assert (meta['omero']['channels'][i]['window']['end'] == clims[i][1])